In Greater Tokyo, many people commute by train between the suburbs and downtown Tokyo for 1 to 2 h per day. The spread of influenza in the suburbs of Tokyo should be studied, including the role of commuters and the effect of government policies on the spread of disease. We analyzed the simulated spread of influenza in commuter towns along a suburban railroad, using the individual-based Monte Carlo method, and validated this analysis using surveillance data of the infection in the Tokyo suburbs. This simulation reflects the mechanism of the real spread of influenza in commuter towns. Three measures against the spread of influenza were analyzed: prohibition of traffic, school closure, and vaccination of school children. Prohibition of traffic was not effective after the introduction of influenza into the commuter towns, but, if implemented early, it was somewhat effective in delaying the epidemic. School closure delayed the epidemic and reduced the peak of the disease, but it was not as effective in decreasing the number of infected people. Vaccination of school children decreased the numbers not only of infected children but also of infected adults in the regional communities.